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One binding site is that of dihydrotetrabenazine (DTBZ). Lobeline binds at this site. Dextroamphetamine and dextromethamphetamine bind at distinct sites to the VMAT2, inhibiting its function. Although the amphetamines inhibit VMAT2 presynaptically leading to diminished neurotransmitter, the primary mechanism for the enhancement of extracellular monoamines, like dopamine, is reversal of the dopamine transporter (DAT).[3]

VMAT2 is essential in the presynaptic neuron's ability to facilitate the release of neurotransmitters into the synaptic cleft. If VMAT2 function is inhibited or compromised, neurotransmitters, such as dopamine, cannot be released via normal transport (exocytosis, action potential) into the synapse. VMAT2 function inhibition can have many various effects on neurotransmitter function, specifically, of importance is its effect on the neurotransmitter dopamine. Dopamine, specifically, is highly neurotoxic to most cellular structures, due to its ability to auto-oxidize in the presence of oxygen radicals. Dopamine, and other neurotransmitters, are metabolized via various processes into various substances, by enzymes such as monoamine oxidase (MAO), catechol-O-methyl transferase (COMT), and dopamine beta hydroxylase (DBH). Vesicles normally protect dopamine from auto-oxidation and metabolism by monoamine oxidase and COMT. Impaired VMAT2 function/activity may contribute to symptoms of depression, anxiety, restless leg syndrome, akathisia, Parkinson's disease, social anxiety, and many other conditions, via inhibition of normal dopamine release into the synapse. Long-term use of amphetamine and methamphetamine causes long-lasting reductions in VMAT2 expression/activity, similar to chronic use of cocaine. This reduction of VMAT2 activity contributes significantly to the neurotoxic effects of amphetamine and methamphetamine. Cocaine users display a marked reduction in VMAT2 immunoreactivity. Sufferers of cocaine-induced mood disorders displayed a significant loss of VMAT2 immunoreactivity, this might reflect damage to dopamine axon terminals in the striatum. These neuronal changes could play a role in causing disordered mood and motivational processes in more severely addicted users.[4]

Mice bred without VMAT2 display marked depression and hypoactivity symptoms, and die within a few days of birth. Their brains exhibit a significant decrease of monoamine and catecholamine content, compared to wild-type mice. Depolarization does not normalize behavior in VMAT2-KO mice, compared to wild-type mice. Amphetamine, however, decreases the functional deficits caused by VMAT-deletion, indicating that monoamines/catecholamines, such as dopamine, are still present in the presynaptic cytoplasm, but not packaged into vesicles necessary for normal depolarization/exocytosis-induced release. In wild-type mice and humans, amphetamine inhibits VMAT2 function and reverses the dopamine transporter (DAT), causing the release of unprotected free cytoplasmic dopamine into the synaptic cleft. VMAT-2 deletion mimics the VMAT-2 inhibition caused by amphetamine, allowing amphetamine to simply reverse the DAT, releasing dopamine, and subsequently reducing functional deficits in VMAT2-KO mice. VMAT2-KO mice also display significantly increased neurotoxicity in response to amphetamine, due to the unprotected metabolism and auto-oxidation of dopamine in the presynaptic cytoplasm of dopamine neurons.[5][6]

Geneticist Dean Hamer has suggested that the VMAT2 gene correlates with spirituality using data from a smoking survey, which included questions intended to measure "self-transcendence". Hamer performed the spirituality study on the side, independently of the National Cancer Institute smoking study. His findings were published in the mass-market book The God Gene: How Faith Is Hard-Wired Into Our Genes.[7][8] However Hamer's claim that the VMAT2 gene contributes to spirituality is controversial.[9] Hamer's study has not been published in the peer reviewed literature and the correlation is not statistically significant.[10]